For them it could have been worse, but for Brazillian keeper Adriano Basso who brought up a one-handed penalty save minutes before the break.
Tommy Smith had been tripped and Watford's top scorer Darius Henderson had stepped up eagerly anticipating his season's 13th goal.
But Basso got it right as he dived to his left to push the ball away, but Henderson will know his shot should have carried more power.
The top of the table clash drew in City's best gate of just over 19,000, but the action never matched the billing on a dour night, won really by the weather.
After their goalless draw at Leicester, the home side made four changes, three of them in defence where Hungarian centre-back, Tamas Vasko, came in late for the injured Jamie McCombe.
Watford brought in Collins John, the Dutchman on loan from Fulham, for Nathan Ellington, but his partnership with Henderson never quite gelled.
There were few moments to worry Basso and when his own midfield at last hit their stride, Watford's keeper Richard Lee twice had to throw himself down to push a 25-yard shot from Marvin Elliott around his right post.
Tension gripped both sides in the swirling rain and it erupted after Henderson's penalty miss.
The frustration was too much for Henderson, who picked up a yellow card for a bad tackle on Lee Johnson. Johnson reacted minutes later, charging into a Danny Shittu to collect a card of his own.
Players were milling around while the fourth official had to step in between the two dug-outs.
City manager Gary Johnson took his son Lee off at the break, replacing him with Australian Nick Carle.
John, who had taken something of a buffeting off Vasko, followed seven minutes into a second period which quickly settled in to the pattern of the first half, but without the same degree of ill-feeling.